Hello all,
I am trying to calculate the h-bond life time using the h-bond command
in cpptraj of Amber 14.
Command I used
*hbond out hbd2l.out donormask :2-22 acceptormask :1&!.H avgout hbd2l.dat
series *
Output looked something like this
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
MOL_1.O3 DG5_2.HO5' DG5_2.O5' 30506 0.6101
2.7374 160.0488
MOL_1.O1 DC_11.H42 DC_11.N4 22038 0.4408
2.8489 160.2850
MOL_1.O1 DC_11.H41 DC_11.N4 7040 0.1408
2.8204 157.7933
MOL_1.N6 DG_13.H22 DG_13.N2 3242 0.0648
2.9357 154.6688
.
.
.
I assumed the fraction to be the life time. That means 0.61 implies 61% of
total frames
To verify this, alternatively I calculated the distance between atoms and
angles separately using cpptraj. Then, using excel, I made an adjoint set
where the dist<3.0 and angle>135 which are defaults. But then the
percentage of frames that satisfy these conditions exceeded significantly
compared to the fraction given by cpptraj. Also the average angle and avg
distance didn't match.
Any idea on how these disparities are coming ?
Any help would be appreciated.
Thanks
--
*Regards, *
*Praneeth Bommisetti, *
*Fourth year Undergraduate,*
*Integrated M.Sc Chemistry, *
*Indian Institute of Technology Bombay.*
*T: +918424815358, id:praneeth.b.iitb.ac.in <id%3Apraneeth.b.iitb.ac.in>*
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Received on Wed Sep 28 2016 - 23:30:02 PDT
